Experiment: 6DK2

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5J5U

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	277	1.5 M ammonium sulphate, 50 mM Tris-HCl pH 7.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 101.703	α = 90
b = 140.269	β = 90
c = 186.63	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	RAYONIX MX-300		2015-11-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.979	APS	21-ID-F

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.02	56.93	99.71	0.085	0.093	0.997	11.13	6.2		172008			35.74

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.02	2.094	99.99		0.521	0.914	2.27	6.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5J5U	2.02	56.93	163616	8392	98.69	0.1528	0.1516	0.16	0.1761	0.19	RANDOM	43.579

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
0.98			-0.45		-0.53

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.058
r_sphericity_free	31.514
r_sphericity_bonded	16.714
r_dihedral_angle_4_deg	16.359
r_dihedral_angle_3_deg	12.013
r_dihedral_angle_1_deg	5.851
r_angle_refined_deg	0.921
r_angle_other_deg	0.834
r_rigid_bond_restr	0.704
r_chiral_restr	0.047

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.058
r_sphericity_free	31.514
r_sphericity_bonded	16.714
r_dihedral_angle_4_deg	16.359
r_dihedral_angle_3_deg	12.013
r_dihedral_angle_1_deg	5.851
r_angle_refined_deg	0.921
r_angle_other_deg	0.834
r_rigid_bond_restr	0.704
r_chiral_restr	0.047
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8220
Nucleic Acid Atoms
Solvent Atoms	984
Heterogen Atoms	184

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
xia2	data reduction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.